title: KAT6A acetylation of SMAD3 regulates  tumor metastasis in triple-negative breast cancer

city: Shanghai

first: Haizhong

last: Feng

state: Shanghai

address: Pujian Road 160

department: Ren Ji Hospital

institute: Shanghai Jiao Tong University

summary: Aberrant SMAD3 activation has been implicated as a driving event in cancer metastasis. However, the drivers of SMAD3 activation are poorly defined. Here, we identify SMAD3 as a non-histone substrate of lysine acetyltransferase 6A (KAT6A). The acetylation of SMAD3 at K20 and K117 by KAT6A with promotes SMAD3 association with oncogenic H3K23ac reader TRIM24 and upregulation of immune response-related cytokines. This event in turn leads to enhanced myeloid-derived suppressor cell (MDSC) recruitment and triple-negative breast cancer (TNBC) metastasis. Inhibiting KAT6A in combination with anti-PD-L1 therapy in treating breast cancer xenograft-bearing animals markedly attenuates TNBC metastasis and provides a significant survival benefit. Thus, our work presents an KAT6A acetylation-dependent regulatory mechanism governing SMAD3 oncogenic function and provides insight into how targeting an epigenetic factor with immunotherapies enhances the anti-metastasis efficacy.

overall_design: Examination of differential gene expression in MDA-MB-231 cells transducted with SMAD3 wild type (WT) or the K20/117Q  (2KQ) mutant


title: Next Generation Sequencing Facilitates Quantitative Analysis of differentially expressed genes between wild type and the fiber mutant Xuzhou142fl

status: Public on Nov 03 2021

city: Linyi

first: Lichen

last: Wang

address: shuangling Rd, middle section

country: China

institute: Linyi University

type: Expression profiling by high throughput sequencing

summary: Tetraploid cotton plants serve as prime natural fiber source for the textile industry. Although various omics studies have revealed molecular basis for fiber development, a better understanding of transcriptional regulation mechanism regulating lint fiber initiation is necessary to meet global natural fiber demand. Here, we aimed to perform transcriptome sequencing to identify DEGs (differentially expressed genes) in ovules of the cotton variety Xu142 and its fibreless mutant Xu142fl during early lint fiber initiation period. Totally, 5516 DEGs including 1840 upregulated and 3676 downregulated were identified. GO enrichment analysis revealed that the downregulated DEGs mainly associated with biological processes such as transcription related biosynthesis and metabolism, organic cyclic compound biosynthesis and metabolism, photosynthesis, and plant cell wall organization, with molecular functions involving transcription related binding, organic cyclic compound binding, and dioxygenase activity, while the upregulated DEGs were associated with DNA replication and phospholipid biosynthetic related processes. Among the 490 DEGs annotated as transcription factor genes 86.5% were downregulated in the mutant including the Malvaceae-specific MMLs, expression patterns of which were confirmed during the central period of lint fiber initiation. Investigation of the 20 genes enriched in the cell wall organization revealed that 17 were EXPA coding genes. Overall, we suggest that lint fiber initiation is a complicated process involving cooperation of multiple transcription factor families, which ultimately lead to the reorganization of the cell wall and terminated cell division of the differentiating fiber initials.

overall_design: mRNA profiles of  mixed ovules at -3 and -1 dpa for wild type (WT) and its fiberless mutant Xuzhou142fl, each contain 3 replicates.


title: Identification of an Enhancer RNA for EGFR in Hyper-accessible Regions in Esophageal Squamous Cell Carcinoma Cells by Analysis of Chromatin Accessibility Landscapes

status: Public on Nov 04 2021

city: Dallas

first: Adwait Amod

last: Sathe

state: Texas

address: 5323 Harry Hines Blvd.

department: McDermott Center of Human Growth and Development

country: USA

institute: UT Southwestern Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To reveal the modified gene regulatory elements including transcription factors and enhancers in esophageal squamous carcinoma cells (ESCC), we performed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) with two ESCC cell lines, i.e. KYSE-30 and KYSE-150, and a non-cancerous esophageal epithelial cell line, HET-1A. This data showed that hyper-accessible regions in ESCC cells contained genes related with cancer hallmarks including DNA replication and angiogenesis. Further motif analysis suggested that AP-1 family transcription factors bind the hyper-accessible regions in KYSE-30 cells as compared to those in HET-1A cells.

overall_design: ATAC-seq libraries from two biological replicates of ESCC cell lines and non-cancer cell HET-1A were prepared separately and sequenced.

first: Sangyong

last: Choi

first: Adwait

middle: A

first: Ewy

last: Mathe

first: Chao

last: Xing

first: Zui

last: Pan


title: Transcriptomic analysis of porcine granulosa cells cocultured with COCs and exposed to the high level of NEFAs during IVM

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

summary: The transcriptome pattern in cocultured granulosa cells that exposed to the high level of NEFAs duing IVM was investigated. Genome-wide transcriptome analysis was performed by microarray using EDMA platform.

overall_design: Two-conditions experiment,  4 replicates of granulosa cells from 4 IVMs

first: Meihong

last: Shi


title: Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells [WGBS]

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

type: Methylation profiling by high throughput sequencing

summary: Human induced pluripotent stem cells (hiPSCs) show variable differentiation potential due to their epigenomic heterogeneity, whose extent/attributes remain unclear, except for well-studied elements/chromosomes such as imprints and the X chromosomes. Here, we show that seven hiPSC lines with variable germline potential exhibit substantial epigenomic heterogeneity, despite their uniform transcriptomes. Nearly a quarter of autosomal regions bear potentially differential chromatin modifications, with promoters/CpG islands for H3K27me3/H2AK119ub1 and evolutionarily young retrotransposons for H3K4me3. We identify 145 large autosomal blocks (≥100 kb) with differential H3K9me3 enrichment, many of which are lamina-associated domains (LADs) in somatic, but not in embryonic stem cells. A majority of these epigenomic heterogeneities are independent of genetic variations. We identify an X-chromosome state with chromosome-wide H3K9me3 that stably prevents X-chromosome erosion. Importantly, the germline potential of female hiPSCs correlates with X-chromosome inactivation. We propose that inherent genomic properties, including CpG density, transposons, and LADs, engender epigenomic heterogeneity in hiPSCs.

overall_design: Examination of epigenetic heterogeneity among human iPSC lines

first: Shihori

last: Yokobayashi

first: Masato

last: Nakagawa

first: Keisuke

last: Okita

first: Bo

last: Hu

first: Yusuke

last: Murase

first: Tomonori

last: Nakamura

first: Guillaume

last: Bourque

first: Jacek

last: Majewski

first: Takuya

last: Yamamoto

first: Mitinori

last: Saitou


title: TNFRSF4-expressing regulatory T cells promote immune escape of chronic myeloid leukemia stem cells

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

summary:
Purpose: The goal of this study was to compare transcriptome profile of FACS-purified bone marrow (BM) Tregs isolated from CML or naive mice.
Methods: Transcriptomic profiles of BM Tregs from CML or naïve mice were assessed in biological replicates using Illumina NextSeq 500.
Results: We mapped around 30 million sequence reads per sample to the mouse genome (GRCm38 - mm10) and identified expressed transcripts in FACS-purified BM Tregs isolated from CML or naive mice. RNA-seq data confirmed stable expression of known housekeeping genes. Differentially expressed genes between Tregs derived from the BM of CML and naïve mice were identified.
Conclusions: Our study represents the first detailed RNA-seq analysis of FACS-purified BM Tregs isolated from CML or naive mice. Our results show that Tregs derived from the BM of CML mice have an increased metabolic activity, cell cycle activity and immunosuppressive capacity.

overall_design: BM Tregs from CML or naive mice were then isolated for RNA extraction and profiled using Illumina NextSeq 500.

first: Magdalena

last: Hinterbrandner

first: Carsten

last: Riether


title: Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells [RNA-seq]


title: Identification of JMJD1A and JMJD2B target genes in renal cell Carcinoma

city: chengdu

first: Lei

last: Qiu

state: sichuan

address: No. 17, Section 3, Renmin South Road

department: Department of General Surgery, Frontiers Science Center for Disease-related Molecular Network, and Cancer Center, West China Hospital

institute: sichuan university

summary:
The Hypoxia-Inducible Factors induce the expression of the histone demethylases JMJD1A (KDM3A) and JMJD2B (KDM4B), linking the hypoxic tumor microenvironment to epigenetic mechanisms that may foster tumor progression. Using transcript profiling, we have identified genes that are regulated in RCC4 with siRNA-mediated knockdown of JMJD1A and JMJD2B.
This dataset includes expression data obtained from renal cell Carcinoma being  loss or mutation of the von Hippel-Lindau (VHL) tumor suppressor gene combination with siRNA-mediated knockdown of  histone demethylases JMJD1A and JMJD2B.

overall_design:
9 samples were analyzed. The log2-transformed normalized signal intensities were used for downstream pairwise comparisons (using Partek Genomic Suite):
SiControl>SiJMJD1A;
SiJMJD1A>SiControl;
SiControl >SiJMJD2B ;
SiJMJD2B>SiControl;

first: Adam

middle: J

last: Krieg


title: Paths and Pathways that Generate Cell-Type Heterogeneity and Developmental Progression in Hematopoiesis

city: Los Angeles

first: Juliet

last: Girard

state: CA

address: 610 Charles E Young Dr E

institute: University of California Los Angeles

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Bulk RNA sequencing on sorted blood cells from Drosophila lymph glands [MZ IZ bulk RNA-seq]

summary: We report the use of bulk mRNA sequencing on FACS-sorted blood cells to identify new and unique genetic markers for each major zone of the  Drosophila lymph gland. We used flow cytomotery in a wild-type genetic background whihc contains two fluorescent reporters that allow for the separation of 4 distinct populations.  Progenitors of the medullary zone (MZ) are marked by dome-meso-EGFP expression. Differentitating cels of the cortical zone (CZ) are marked by Hml-DsRed. These two sorted populations (MZ and CZ) are positive for the expected zone-specific markers (i.e. Tep4,  dome, and shg for MZ and Hml, Pxn, vkg, Col4a1, and NimC1 for plasmatocytes of the CZ), however, the CZ population also expresses crystal cell markers (hnt, lz, ProPO), indicating that it is a mix of plasmatocytes and crystal cells. Intermediate progenitors of the intermediate zone (IZ), which are not well understood and do not have specific markers, but are characterized by simultaneous expression of EGFP and DsRed (double positives) were also sorted. In addtiion, there is a population of lymph gland cells that is double negative for both EGFP and DsRed fluorescence. This double negative population contains a mix of cell types including posterior signaling center (PSC) cells, MZ and CZ cells that have lost fluorescence, late crystal cells that do not express Hml (early CCs do express), and non-blood cells (i.e. dorsal vessel and pericardial cells). These double negatives were excluded from the analysis for these reasons. We analyzed transcript data of these 4 sorted populations in the early third instart larvae (90-96 hours after eggs lay at 25 degrees C). We identified novel markers that are differentially expressed in each of the three major blood cell populations (MZ, IZ, CZ) that have been useful to definetely identify populations in scRNA-Seq and give information about transcript isoforms in each of the distinct populations.

overall_design: Examination of mRNA expression in sorted  blood cell populations

middle: R

first: Lauren

middle: M

last: Goins

first: Dung

last: Vuu

first: Utpal

last: Banerjee


title: Single cell RNA-sequencing on blood cells from Drosophila lymph glands [scRNA-seq]

summary: We report the use of single cell mRNA sequencing to identify new blood cell types, subtypes, genetic markers, and important developmental pathways in the Drosophila lymph gland. We analyzed transcript data for 21,157 cells from wild-type early third instar larvae (90-93 hours after eggs lay at 25 degrees C) which contain reporter constructs that mark progenitors and differentiated cells. We find that lymph gland blood cells can be catorgorized into 9 major clusters. One cluster corrresponds to the niche cells of the posterior signaling center (PSC) that expressed the PSC markers Antennopedia and Collier. Progenitors of the medullary zone (MZ) are found in two distinct clusters (MZ1 and MZ2), both of which express the MZ markers domeless and Tep4. One cluster contains intermediate progenitors of the intermediate zone (IZ), and these express markers such as CG30090, lectin-24A, and MFS3 that we found to be IZ-specific in previous bulk RNA-seq experiments with sorted lymph gland cells. Another cluster (PL) contains plasmatocytes that express NimC1, as well as Hml, Pxn, vkg, and Col4a1. Crystal cells are found in one major population that subclusters into two distinct subclusters (CC1 and CC2) that express the markers lz, Hnt, and proPO.. Another transitory population that we dub proplasmatocytes expresses Hml, Pxn, vkg, and Col4a1, but not PL marker Nimc1 or IZ-markers. One cluster is not well understood, butis highly enriched for cell cycle- and replication stress genes. Pseudotime and Trajectory analysis results in fruther sub-division of these zones based on pseudotime states and aids in building a model of lymph gland development that will be the basis for future studies.

overall_design: Examination of mRNA expression in blood cells


title: NR4A1 suppresses cancer replication stress through R-loop-dependent inhibition of immediate early gene transcriptional elongation [ATAC-seq]

city: Boston

first: Gabriel

middle: Alejandro

last: Golczer Gatti

state: MA

address: 55 Fruit St

department: MGH Cancer Center

institute: Harvard Medical School

summary: Deregulation of oncogenic proliferative signals triggers replication stress in cancer cells to which they must adapt. Immediate early genes (IEGs), identified by their rapid stress-induced transient bursts of expression, are critical to integrating downstream signaling pathways. In studying tumor initiation by patient-derived breast cancer cells, we observed acquisition of open chromatin domains at the genebody and 3’-UTR of IEGs, uniquely across the genome. Through in vivo and in vitro modeling, we show that the IEG and orphan nuclear receptor NR4A1 localizes across multiple IEG genebodies, where it binds to RNA Pol II, arresting transcriptional elongation and generating extensive R-loops and accessible chromatin. Acute stress promptly removes NR4A1 from IEG genebodies, triggering immediate release of their poised transcripts. In breast cancer cells, NR4A1 overexpression increases tumorigenesis; conversely, its deletion leads to uncompensated replication stress, chromosomal instability and mitotic catastrophe, driven by deregulation of its IEG target FOS. A large fraction of primary breast and other cancers exhibit open genebody chromatin at IEGs, consistent with preserved NR4A1 function. Thus, NR4A1 mediates a novel transcriptional elongation checkpoint, unique to stress-induced genes and required for their rapid bursts of expression. Cancers that have retained this mechanism in adapting to chronic replication stress may be dependent on NR4A1 for proliferation.

overall_design: In this study, we sequenced 12 ATAC-seq samples, including 4 samples of BRx142 CTC cells, 4 samples of BRx82 CTC cells and 4 samples of MCF10A cells with or without RNAseH1 overexpression.

first: Hongshan

last: Guo

last: Golczer

first: Ben

middle: S

last: Wittner

first: Shyamala

last: Maheswaran

first: Michael

last: Lawrence

first: Daniel

last: Haber


title: Bulk RNA sequencing on sorted blood cells from Drosophila lymph glands [PL iCC mCC bulk RNA-Seq]

summary: We report the use of bulk mRNA sequencing on FACS-sorted blood cells to identify new and unique genetic markers for each major differentiated cell type of the Drosophila lymph gland. We used flow cytomotery in a wild-type genetic background whihc contains two fluorescent reporters that allow for the separation of 3 distinct populations. Plasmatcytes express the markers Hml, Pxn, vkg, Col4a1, and NimC1 , while crystal cells are markered by expression of hnt, lz, ProPO. mCC has higher expression of ProPO relitive to iCC, but lower expression of Hml and DsRed. We identified novel markers that are differentially expressed in each of the three major differentiated blood cell populations (PL, iCC, and mCC) that have been useful to definetely identify populations in scRNA-Seq and give information about transcript isoforms in each of the distinct populations.

overall_design: Examination of mRNA expression in sorted blood cell populations


title: NR4A1 suppresses cancer replication stress through R-loop-dependent inhibition of immediate early gene transcriptional elongation [bulk RNA-seq]

overall_design: In this study, we sequenced 5 bulk RNA-seq samples from two groups. One group has 3 biological replicates, another group has 2 biological replicates.


title: Sperm transcriptome of infertile men

city: Prague

first: Lukáš

middle: Farhád

last: Mirchi

state: Czech Republic

address: Albertov 4

department: First Faculty of Medicine

country: Czech Republic

institute: Charles University

summary: Infertility is a widespread health problem, with rising incidence worldwide. Whether the infertility is caused by genetic or environmental factors, the reason for inability to reproduce can be the too low number of sperm or morphological or functional abnormality of the sperm. Therefore there can be a certain possibility that divergent causes would converge in common mechanisms impairing sperm functionality. A key step in the control of the cell phenotype is the regulation of gene expression. Therefore, the sperm transcriptome can reflect the impairment of proper regulatory networks acting during spermatogenesis and later, during sperm maturation. Also, it can be speculated that some sperm RNAs can influence the fitness of the early embryo, despite the small amount of sperm RNA. Although the changes in transcriptome are not always reflected by similar changes in the proteome, a relative ease of transcriptome interrogation makes it an excellent tool for hypothesis generation about infertility mechanisms and for a search for potential infertility biomarkers.

overall_design: We analyzed the transcriptome of 24  sperm samples using Affymetrix HuGene2.1ST microarrays. 6 participants were fertile men with normal sperm parameters, 5 samples were from infertile patients that presented low sperm motility (asthenozoospermia), and 7 samples with low motility as well as abnormal morphology (asthenoteratozoospermia) and 6 were infertile men with no semen abnormality. Differential expression of most significant genes was confirmed by qPCR.

first: Blanka

last: Chylíková

first: František

last: Liška


title: NR4A1 suppresses cancer replication stress through R-loop-dependent inhibition of immediate early gene transcriptional elongation [ChIP-seq]

overall_design: In this study, we sequenced 68 ChIP-seq samples for different cell lines and circulating tumor cells growing in mouse organs after intracardiac injection.


title: Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells [ChIP-seq]

first: Yukihiro

last: Yabuta

first: Shihori

last: Yokobayashi

first: Masato

last: Nakagawa

first: Keisuke

last: Okita

first: Bo

last: Hu

first: Yusuke

last: Murase

first: Tomonori

last: Nakamura

first: Guillaume

last: Bourque

first: Jacek

last: Majewski

first: Takuya

last: Yamamoto

first: Mitinori

last: Saitou


title: Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells


title: Single-cell RNA sequencing of enriched cells from Gli1_Cre_ERT2/WT; Rosa_mTmG/WT mouse

city: Ann Arbor

first: Vibha

middle: N.

last: Lama

state: Michigan

address: 1150 W. Medical Center Drive

department: Internal Medicine

institute: University of Michigan

summary: A single cell transcriptional profile of CD45neg CD31neg cell populations isolated from Gli1_Cre_ERT2/WT; Rosa_mTmG/WT mouse lungs.

overall_design: CD45neg CD31neg cell populations isolated from Gli1_Cre_ERT2/WT;Rosa_mTmG/WT mouse lungs and submitted to the UM DNA Sequencing Core where the cells were checked for viability. The single cell RNA-seq libraries were prepared at the University of Michigan Advanced Genomics Core using the 10X Genomics Chromium Next GEM Single Cell 3′ Kit v3.1 (part number 1000268) following the manufacturer’s protocol. The total number of cells recovered was 11,118.

middle: N

first: Russell

last: Braeuer

first: Natalie

last: Walker

first: Ragini

last: Vittal


title: NR4A1 suppresses cancer replication stress through R-loop-dependent inhibition of immediate early gene transcriptional elongation

first: Gabriel

last: Golczer Gatti


title: Defining the role of NF-ĸB p105/p50 in human macrophage through the transcriptomic analysis of NFKB1 deletion in THP-1 cells

city: Glasgow

first: Domenico

last: Somma

address: 120 University Place

department: Institute of Infection, Immunity & Inflammation

country: United Kingdom

institute: University of Glasgow

summary: Effect of LPS stimulation on WT vs NFKB1-/- human macrophage induced THP-1 cell line

overall_design: Trascriptome of PMA-induced macrophage WT or NFKB1-/- either unstimulated or LPS-stimulated

first: David

last: Kerrigan

first: Christine

last: Wells

first: Ruaidhrí

last: Carmody


title: NR4A1 suppresses cancer replication stress through R-loop-dependent inhibition of immediate early gene transcriptional elongation [DRIP-seq]

overall_design: In this study, DNA:RNA hybrid immunoprecipitation followed by sequencing (DRIP-seq) was carried out for both MDA-MB-231 and MCF10A cells.

first: Hongshan

last: Guo

last: Golczer

first: Ben

last: Wittner

first: Shyamala

last: Maheswaran

first: Michael

last: Lawrence

first: Daniel

last: Haber


title: RNA sequencing (RNA-SEQ) of HMGA1 knockdown by shRNA in cholangiocarcinoma cells

city: Jinan

first: Jianping

last: Song

state: Shandong

address: 107 Wenhua Xi Road, Jinan, Shandong Province, China.

institute: Qilu hospital of Shandong University

summary: Cholangiocarcinoma (CHOL) is a malignancy arising from either the intrahepatic or the extrahepatic bile ducts which carries a severe prognosis. HMGA1 is a transcription factor which has a high expression level in many types of cancer. In this study, we find HMGA1 overexpression in CHOL. In order to investigate the regulatory mechanism of HMGA1 in CHOL, we performed RNA-seq in HUCCT1 cells with HMGA1 knock down compared with control in three repeat.

overall_design: The assay was performed in HUCCT1 cells with HMGA1 knock down and control cells on three biological triplicates .

first: Zhaojina

last: Liu


title: Integrative proteome analyses implicate aberrant RNA splicing impairs developmental potential of aged mouse oocytes

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

summary: Aging has many effects on female reproductive system, among which declined oocyte quality and impaired embryo developmental potential are the most important factors affecting female fertility. However, the mechanisms of oocyte aging have not yet been fully understood due to the complex and multifactorial nature of this physiological process. Here, we selected normal reproductively aging female mice as research object and constructed protein expression profile of metaphase II (MII) oocytes from three age groups. A total of 187 differentially expressed (DE) proteins were identified, and bioinformatics analysis showed that these DE proteins were highly enriched in the RNA splicing. Next, RNA-seq was performed on 2-cell embryos from these three age groups, splicing analysis showed that there were a total of 1375 differentially spliced genes (DSGs) and 2363 differentially spliced events (DSEs). DSGs in the reproductive aging groups versus the younger group were enriched in biological processes related to DNA damage repair/response. Binding motif analysis suggested PUF60 may be the core splicing factor that causes the decline of the developmental potential of oocytes in reproductive aging mice, and changing the splicing pattern of its potential downstream DSG Cdk9 could partially mimic phenotypes in the reproductive aging groups. Taken together, our study suggested the abnormal expression of splicing regulation protein in aging MII oocytes will affect the splicing of nascent RNA after zygotic genome activation in 2-cell embryos, leading to the production of abnormally spliced transcripts of some key genes associated with DNA damage repair/response, thus affected the developmental potential of aged oocytes.

overall_design: Total 14 samples from 8-10w, 6-8m and 10-12m mice from MII oocytes and 2-cell embryos.

first: Mingrui

last: Li


title: NR4A1 suppresses cancer replication stress through R-loop-dependent inhibition of immediate early gene transcriptional elongation [PRO-seq]

overall_design: In this study, Precision nuclear Run-On followed by sequencing (PRO-seq) was carried out for 8 samples from two cell lines, MDA-MB-231 and MCF10A cells.


title: Differentially expressed genes in absence of histone H3K4 methyltransferase Set1 in Candida albicans

city: Chuncheon-si, Gangwon-do

first: Jueun

last: Kim

address: 1 Kangwondaehak-gil

country: South Korea

institute: Kangwon National University

summary: Candida albicans is an opportunistic human fungal pathogen. It exists as a member of human normal flora but can cause infection in immunocompromised individuals. Transition to pathogenic C. albicans requires a change in gene expression of various genes. As the histone-modifying enzymes can regulate gene expression, they can be considered as a factor controlling the virulence of C. albicans. Among them, it has been reported that the absence of H3K4 methyltransferase Set1 reduces the virulence of C. albicans. However, Set1-regulated genes responsible for this attenuated virulence phenotype are unknown. Here, we identified that the Set1 positively regulates the expression of mitochondrial protein genes and oxidative stress response-related genes through the methylation of H3K4. Levels of cellular mitochondrial reactive oxygen species (ROS) in Δset1 are also higher than those in the wild-type. Furthermore, Set1 deletion increases sensitivity to hydrogen peroxide (H2O2). Set1 deleted mutant also does not form its colony properly when it interacts with macrophage in vitro, in agreement with its attenuated virulence in vivo. Therefore, Set1 is required to inhibit cellular ROS production by positive regulation of mitochondrial protein genes and oxidative stress response-related genes expression, and consequently, the Set1-mediated gene expression assists C. albicans in defending against ROS generated from the host more rapidly.

overall_design: mRNA profiles of wild-type and Δset1 were generated by deep sequencing, in duplicate, by Illumina HiSeq 2500

first: Shinae

last: Park

first: Jung-Shin

last: Lee


title: Transcriptome analysis of mice dermal white adipose tissue during aging

city: GuangZhou

first: Qian

last: Qu

address: 1838 North Guangzhou AV

institute: Nanfang Hospital of Southern Medical University

summary: Dermal white adipose tissue (dWAT) is one of the peripheral tissues directly adjacent to hair follicle(HF) and acts as critical macroenvironmental niche of HF. dWAT directly contribute to HF aging by paracrine signals secretion. However, the altered interrelationship between dWAT and HF with aging has not been thoroughly understood

overall_design: Here, through microdissection, we separated dWAT from skin of aged mice (18 months) and young mice (2 months) in telogen and depilation-induced anagen for transcriptome comparing.

first: Zhi-Qi

last: Hu

first: Yong

last: Miao


title: p300 suppresses the transition of myelodysplastic syndrome to acute myeloid leukemia [ChIP-seq II]

city: Miami

first: Stephen

last: Nimer

state: FL

address: 1120 NW 14th ST

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

summary: The p300 lysine acetyltransferase (KAT) can function as an oncogene or a tumor suppressor in hematologic malignancies. We have identified a tumor suppressor role for p300 in myelodysplastic syndrome (MDS) driven by Tet2 deficiency. Compared to Tet2-null hematopoietic stem and progenitor cells (HSPCs), HSPCs lacking both p300 and Tet2 (double knock out, DKO) displayed enhanced proliferation and impaired differentiation. Consequently, p300Δ/Δ Tet2-/- mice developed acute myeloid leukemia. p300 loss in Tet2-/- HSPCs induced a global epigenomic reprogramming that enhanced leukemogenicity at least in part by increasing expression of Myb, as knock-down of Myb specifically hindered the proliferation of the DKO HSPCs. We show that p300 KAT activity regulates the function of Tet2 null HSPCs, and that augmenting p300 function impairs their unlimited self-renewal. Such a strategy could prove useful in individuals with Tet2 deficient hematopoiesis or MDS.

overall_design: 25M mouse lin- bone marrow cells were isolated from WT mice for Myb enrichment by ChIPseq.

first: Man

first: Nimer

last: Stephen


title: p300 suppresses the transition of myelodysplastic syndrome to acute myeloid leukemia [DIP-seq]

overall_design: Genomewide 5hmc enrichment was determined for each sample by antibody IP for 5hmc over input using genomic DNA from sorted mouse HSPCs.  There were three independent replicates per genotype.

last: Man


title: Physiological and molecular responses of 'Dusa' avocado rootstock to water stress: insights for drought tolerance

city: Pretoria

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Lynnwood Road

department: Plant and Soil Science

country: South Africa

institute: University of Pretoria

summary: The aim of this study was to evaluate the physiological response and the expression analysis of `Dusa´ avocado rootstocks subjected to two different levels of water stress, and their subsequent recovery. At the beginning of the experiment, avocado plants were divided in Control plants (watered to field capacity (Fc) throughout the experiment) and stressed plants that were subjected to controlled substrate drying-up until they reached 50% of Fc (mild-WS) and 25% of Fc (severe-WS), respectively. Afterwards, plants were fully irrigated to assess drought recovery response. A set of physiological measurement were taken at leaf and whole-plant levels to assess avocado response to each level of water stress and rewatering. Root samples were collected in mild-WS and severe-WS and gene expression analysis was carried out using a targeted cDNA avocado stress microarray containing transcripts from de novo sequencing of 'Dusa' in response to biotic and abiotic stress. Avocado gene expression profiles under different levels of water stress are discussed in order to shed light on the molecular mechanisms associated with water deprivation in Dusa avocado rootstocks.

overall_design: Direct comparison, three biological replicates control vs stress for Mild-WS, two biological replicates control vs stress for Severe-WS

first: G

last: Moreno-Ortega

first: E

last: Martínez-Ferri

first: A

last: Zumaquero

last: Matas

first: N

last: Olivier

first: F

last: Pliego-Alfaro

last: van den Berg

first: C

last: Pliego


title: Comparative transcriptome analysis of transgenic Drosophila misexpressing novel Notophthalmus viridescens (newt) genes

city: Davis

first: Abijeet

middle: Singh

last: Mehta

state: California

address: Tupper hall

department: Dermatology

institute: University of California

summary: To obtain a quick glimpse into possible function of five novel Notopthalmus viridescens (newt) genes (and given certain restrains with transgenic newts, such as time) we express these genes using transgenic Drosophila melanogaster. We generated the transgenic flies containing newt candidate genes, and prepared samples for RNA sequencing to evaluate the overall role of candidate genes in tissue development and layout map for future studies.

overall_design: We generated five transgenic fly strains each expressing single copy of the five novel Newt genes named as candidate 1 (C1), Candidate 2 (C2), Candidate 3 (C3), Candidate 4 (C4), and Candidate 5 (C5) respectively. Transgenic flies were generated using microinjection-based ϕC31 integrase mRNA-mediated method. A cloned candidate gene using pUAST-attB plasmid containing both a transgene and donor sequence (attB) is coinjected along with ϕC31 integrase mRNA into attP-containing recipient embryos, resulting in the site-specific insertion of the transgene. Sample (total RNA) for RNA sequencing was collected at 3rd instar larval stage during which major developmental events takes place in Drosophila. Total RNA was extracted, and purified using RNA clean and ConcentratorTM, and high quality RNA samples were used for downstream processes e.g. next-generation RNA sequencing. Of the total 36,099 transcripts in Drosophila, 34,967 transcripts were detected, and 2775 transcripts were significantly regulated by misexpressing these unique gene from newt in Drosophila. Genes involved in the developmental process, cell cycle, apoptosis, and immune response are among those that are highly enriched.

first: Agustin

last: Luz-Madrigal

first: Jian

middle: L

last: Li

first: Panagiotis

last: Tsonis

first: Amit

last: Singh


title: Pancreatic cancer cells render metabolic reprogramming of tumor-associated macrophages through a GARP-dependent and DNA methylation-mediated mechanism

city: Hangzhou

first: Mengwen

last: Zhang

state: Zhejiang

address: 88 Jiefang Road

institute: Zhejiang University

summary: We performed whole genome RNA expression analysis by RNA sequencing on M0, M1-like macrophages and M2-like macrophages, respectively, comparing to those following co-culturing with human PDA tumor cells.We focused on the genes in the glucose metabolism pathway and oxidative phosphorylation pathway that were found to be methylated and downregulated in CAFs after co-culturing with PDA tumor cells in our previous experiment. We found that PDA tumor cells induce downregulation of metabolism genes selectively in M1 macrophages than in M2 macrophages.

overall_design: Demonstrate the metabolic reprogramming of PDA cells on M0, M1-like macrophages and M2-like macrophages.

first: Lei

last: Zheng


title: Angiogenesis induced by aminoacyl-tRNA synthetase deficiency is dependent on AAR but not UPR pathways

city: Shanghai

first: Chun-hui

last: Xu

address: 197 Ruijin Road II

department: State Key Laboratory of Medical Genomics

institute: Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine

summary: The amino acid response (AAR) and the unfolded protein response (UPR) pathways are closely interconnected and both implicated in regulation of stress-induced angiogenesis. Two kinases, Gcn2 and Perk, transduce signals from AAR and UPR, respectively, and phosphorylate the common target, eIF2alpha, the key regulator of protein translation. However, this interconnection makes it difficult to specify different contributions of AAR and UPR to angiogenesis. In this study, we generated a zebrafish angiogenic model harboring a loss-of-function mutation in the threonyl-tRNA synthetase (tars) gene. While previous studies approximately implicated both AAR and UPR into the angiogenic phenotypes, our gene expression profiling of the tars-/- and sibling embryos, as well as those with knockdown of either Gcn2 or Perk in both genotypes, reveal that only AAR is activated by the tars-deficiency. Phenotypic validations using genetic and pharmacological interference with AAR and UPR confirm that AAR, but not UPR, is required for the tars-deficiency-induced angiogenesis. Thus, this study demonstrates that the closely interconnected AAR and UPR can be independently activated and differentially regulate angiogenesis, which reflects the specificity and efficiency of multiple stress response pathways that are evolved integrally to benefit the organism by ensuring sensing and responding precisely to different types of stress.

overall_design: The six samples, including uninjected WT or tars-/- embryos, as well as those with either perk MO or gcn2 MO injected embryos in both genotypes, were subjected to RNA-seq analysis.

first: Fan

first: Chun-Hui

first: Xiao-Jian

last: Sun


title: Attention to time-of-day variability improves the reproducibility of gene expression patterns in multiple sclerosis

city: Hong Kong

first: KIM

last: Jin Young

address: Tat Chee Avenue, Kowloon, Hong Kong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: Most biomarkers for the diagnosis and prognosis of multiple sclerosis (MS) are not yet clinically available due to low reproducibility. Here, we show that times of day affect gene expression profiles in MS patients. Thus sample collection has to be standardized based on the time-points biomarkers are expressed to increase reproducibility. In this study, we examined transcriptome profiles in whole blood of MS patients collected at two different time-points of the day, around 2 pm as the daytime and 9 pm as the nighttime. We observed the significantly changed gene expression profiles in the relapsing patients at nighttime compared to their daytime samples and the remitting patients at nighttime. Among all DEGs, we focused on differentially expressed genes (DEGs) related to immune responses because of association with clinical outcomes of MS. 68 immune responses-associated DEGs significantly changed their expression in the relapsing patients at nighttime but not in their daytime samples and remitting patients at nighttime. Therefore, this study shows that: 1) gene expresion patterns in relapsing patients are changed compared to remitting patients; 2) altered gene expression patterns in relpasing patients are detected at nighttim; 3) times of day to collect samples from MS patients should be standardized based on the gene expression patterns across a day.

overall_design: Seven relapsing-remitting multiple sclerosis (RRMS) patients and three healthy controls who had no history of neurological or psychiatric diseases were recruited. Whole blood was collected two times a day from all individuals:  2 pm (daytime) and 9 pm (nighttime), using the PAXgene Blood RNA tubes. Total RNA was extracted using the PAXgene Blood RNA Kit (all from QIAGEN) and subjected to RNA-sequencing analysis to obtain the gene expression profiles.

first: Jin

last: Kim

first: Xin

last: Wang

first: Suihong

last: Huang

first: Tan

last: Wu

first: Alexander

middle: Y

last: Lau

first: Cheryl

last: Au

first: Hao


city: Baltimore

state: Maryland

address: 1650 Orleans Street, CRB I Rm 351

department: Department of Oncology

institute: Johns Hopkins University

summary: Genome wide DNA methylation profiling of cancer associated macrophages. Results showed DNA methlation status in M0 and M1-like macrophages changed after coculture with pancreatic cancer cells, but not in M2-like macrophages.

overall_design: M0, M1-like and M2-like macrophages either cultured alone or co-cultured with pancreatic tumor cells then purified by anti-CD11b antibody coupled microbeads. DNA were abtained, DNA methylation were compared between cultured alone and cocultured.


title: p300 suppresses the transition of myelodysplastic syndrome to acute myeloid leukemia [ATAC-Seq]

first: Stephen

last: Nimer

overall_design: ATACseq was performed on 50,000 HSPCs sorted from mouse bone marrow samples.

last: Man


title: Genome wide expression change by TRIM56 knocking down in MCF-7 cells

city: Shenzhen

first: Qiangzu

address: Nan Hai Da Dao Chuang Shi Ji Bin Hai Hua Yuan Building9 9A , Nanshan District, Shenzhen City, Guangdong Province

institute: Lemondata BioTechnology Limited

summary: We aim to the investigate the role of TRIM56 in breast cancer progression. MCF-7 cells were used as the model and TRIM56 was silenced by siRNA.

overall_design: The MCF-7 cells were treated with 50nM scramble siRNA and siTRIM56. After 48 hours, cells were harvested and the total RNA was extacted by Qiagen kit. The RNA sample was sent to BGI for RNA expression anaylsis.

first: jian

last: zhu

first: Hui

last: wang


title: p300 suppresses the transition of myelodysplastic syndrome to acute myeloid leukemia [RNA-Seq]

overall_design: RNAseq was performed on 1-2x10^5 sorted LSK cells from 8-10 week old Mx1-Cre+ WT, Ep300f/f, Tet2-/-, or Ep300f/f;Tet2-/- mice, 2 weeks after poly(I:C) injections.


title: Depleting ribosomal RNA sequencing of urine-derived ADO2-iPSCs.

first: Minglin

last: Ou

address: No.1017, Dongmen North Road, Luohu District

department: Clinical Medical Research Center of The Second Clinical Medical College

institute: Jinan University

summary: To construct comprehensive competing endogenous RNA (ceRNA) networks , depleting ribosomal RNA strand-specific libraries  were constructed from the ADO2-iPSCs and normal control human iPSCs (NC-iPSCs) for deep RNA sequencing.

overall_design: RNA sequencing was performed for the identification and expression profiles of circRNAs, lncRNAs and mRNAs between the ADO2-iPSCs and NC-iPSCs libraries.

first: Chunhong

last: Li


title: p300 suppresses the transition of myelodysplastic syndrome to acute myeloid leukemia

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Changes in gut microbiota induced by oral pathobiont deteriorate the pathology of non-alcoholic fatty liver disease

city: Niigata

first: Kazuhisa

last: Yamazaki

address: 2-110-1 Gakkocho-dori, Chu-o-ku

institute: Niigata University

summary: Periodontitis increases the risk of non-alcoholic fatty liver disease (NAFLD). However, the precise mechanisms are unclear. Here, gut dysbiosis induced by orally administered Porphyromonas gingivalis, a representative periodontopathic bacterium, was implicated in the deterioration of NAFLD pathology. C57BL/6 mice were administered with the vehicle, P. gingivalis or Prevotella intermedia, with weaker periodontal pathogenicity, followed by feeding on a choline-deficient, high fat diet (CDAHFD60). CDAHFD60 feeding induced hepatic steatosis, and combined bacterial administration further aggravated NAFLD pathology with increased fibrosis. Liver gene expression analyses revealed that genes involved in the NAFLD pathology were perturbed with distinctive expression profiles induced by different bacteria. These differences may be due to quantitative and qualitative differences in the influx of gut bacterial products because the serum endotoxin level, gut microbiota composition, and serum metabolite profile caused by ingested P. intermedia and P. gingivalis were different. These findings provide insights into mechanisms linking periodontitis and NAFLD.

overall_design: Effect of oral administration of P. intermedia and P. gingivalis on the liver gene expression profile was mesured in high fat diet-fed mice. Mice were divided into 4 groups ( regular chow, no bacteria (n=3), high fat diet, sham (n=4), high fat diet, P. intermdia (n=4), high fat diet, P. gingivalis (n=5)). Bacteria were administered 2 times aweek for 3 weeks nd high fat diet was fed for 2 weeks.

first: Kyoko

first: Nobuaki

last: Miura

first: Shujiro

last: Okuda

first: Tamotsu

last: Kato


title: Genome-wide binding profile of EBF1 in B cells.

status: Public on Nov 02 2021

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: EBF1 ChIPSeq of CD19+ B cells

overall_design: EBF1 ChIP was performed on CD19 + primary B cells obtained from 3 healthy individuals.

first: Sören

last: Boller

first: Roshni

last: Roy

first: Ranjan

last: Sen

first: Rudolf

last: Grosschedl


title: Small RNA sequencing of urine-derived ADO2-iPSCs

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify potential miRNA–mediated targets associated with osteopetrosis at the genome-wide level, two small RNA libraries and a degradome library were constructed from the ADO2-iPSCs and normal control human iPSCs (NC-iPSCs) for deep sequencing.

overall_design: Small RNA sequencing was performed for the identification and expression profiles of miRNAs between the ADO2-iPSCs and NC-iPSCs libraries.


title: Mitochondrial matrix protein C14orf159 attenuates colorectal cancer metastasis through suppression of Wnt/β-catenin signaling

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Despite the progression in understanding the molecular events in colorectal tumorigenesis, the mechanisms underlying metastasis remain unclear. Recently, altered metabolism including mitochondrial function of cancer cells has emerged as an important factor which regulates metastatic capability of cancer. Here, we show that mitochondrial matrix protein C14orf159 attenuates colorectal cancer metastasis by suppressing Wnt/β-catenin signaling. We demonstrated that C14orf159 maintained mitochondrial membrane potential of human colorectal cancer cells and was involved in amino acids and glutathione metabolism. In human colorectal cancer specimens, expression of C14orf159 was decreased in the tumor invasive fronts and metastatic lesions. C14orf159 attenuated the capability of migration, invasion and spheroid growth in colorectal cancer cells in vitro and colorectal tumor growth and metastasis in vivo. Mechanistically, C14orf159 reduced expression of the genes involved in colorectal cancer metastasis including WNT and MMP family partly by maintaining mitochondrial membrane potential. These findings provide a new link between mitochondrial membrane potential and Wnt/β-catenin signaling, and uncover the novel function of the mitochondrial matrix protein C14orf159 as a suppressor in colorectal cancer metastasis.

overall_design: To explore why C14orf159 decreases migration and invasion capability and spheroid growth in human colorectal cancer cells, we conducted RNA-seq analysis in C14orf159-KO and control HCT116 cells.

first: Kenji

last: Ohshima

first: Eiichi

last: Morii


title: An expansion of genomic regulatory complexity underlies vertebrate neuronal diversity

city: New York

first: Michael

last: Closser

institute: Columbia University

summary: The proper assembly and function of the mammalian nervous system requires the generation of a uniquely diverse population of neurons. Neuronal identity can be viewed as a cell-type-specific combination of broadly expressed effector genes (e.g. receptors, cytoskeletal proteins, adhesion molecules, ion channels, neurotransmitters) that collectively define neuronal morphology, connectivity, and function. How countless, partially overlapping, yet cell-type-specific patterns of gene expression are controlled at the genomic level remains poorly understood. Using primary and stem cell-derived motor neurons, we mapped enhancer-promoter interactions, revealing that motor neuron enhancers are distributed across large chromatin domains, instead of clustered as super-enhancers previously described in other tissues. The distributed enhancers converge on promoters to regulate both neuronal cell-type- and cell-stage-specific patterns of gene expression. Distributed dynamic enhancers are not a unique property of motor neurons, but are broadly employed in the regulation of gene expression throughout the nervous system. Together, our findings establish that neuronal genes are associated with expanded non-coding genomic domains, accommodating large numbers of independent cell-type- and cell-stage-specific regulatory elements. This regulatory system facilitates the implementation of complex gene expression programs underlying the expansion in the cellular diversity of the vertebrate central nervous system.

overall_design: Genomic maps of regulatory elements in different neuronal cell types

first: Hynek

last: Wichterle


title: Specification of human immune cell epigenetic identity by combinations of transcription factors

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: We identify lineage-specific methylation and transcriptomic patterns in 6 primary immune cells from 24 healthy donors. We also look into the association of B cell-specific methylated sites with EBF1 ChIP-Seq binding patterns

overall_design: Identify lineage -specific methylation and transcription patterns in 6 primary immune cells

first: Mary

last: Kaileh

first: Luigi

last: Ferrucci


title: Single-cell functional transcriptomics of mouse DRG mechanosensory neurons

city: Marseille

first: Thibaud

last: Parpaite

address: 51 Bd Pierre Dramard

department: Neural basis of the Somatosensory System

country: France

institute: Aix-Marseille University

summary: A variety of mechanosensory neurons are involved in touch, proprioception and pain. Many molecular components of the mechanotransduction machinery subserving these sensory modalities remain to be discovered. Here, we combined recordings of mechanosensitive (MS) currents in mechanosensory neurons with single cell RNA sequencing. In silico analysis of collected data combined with a previous large-scale dataset allowed to link the four identified kinetically distinct MS current subtypes to transcriptomically defined populations of DRG neurons. Moreover, gene expression differential comparison provided a list of candidate genes for mechanotransduction complexes. This dataset constitutes an open-resource to explore further the cell-type-specific determinants of mechanosensory properties.

overall_design: scRNAseq of mechano-phenotyped DRG neurons using patch-clamp experiments

first: Bertrand

last: Coste


title: p300 suppresses the transition of myelodysplastic syndrome to acute myeloid leukemia [ChIP-seq]

first: Stephen

last: Nimer

overall_design: 25M mouse lin- bone marrow cells were isolated from each genotype (WT, P300KO, TET2KO, P300KO/TET2KO) for H3K27ac enrichment by ChIPseq.  Signal tracks were generated over Histone H3 genome-wide enrichment.

last: Man


title: Systemically administered HMGN1 immunostimulatory peptide with anti-PD-L1 antibody exerts synergistic antitumor effects

city: Boston

first: Alex Chang-Yu

last: Chen

address: 149 13th Street, 7th floor, Room 7103

department: Krantz Family Center for Cancer Research

institute: Massachusetts General Hospital

summary: In this study, we explore a new combination therapy of anti-PD-L1 antibody with an immunostimulatory peptide derived from an alarmin high mobility group nucleosome binding protein 1 (HMGN1). Combination treatement of HMGN1 immunostimulatory peptide  with anti-PD-L1  antibody exerted robust anti-tumor effects in Colon26 subtaneous murine model. To understand transcriptomic differences of  immune cell population in the tumor-bearing mice after treated with  single-agent or combination therapy of HMGN1 with anti-PD-L1 antibody, we performed transcriptome analysis on tumor tissue using 5’end Serial Analysis of Gene Expression (SAGE)-sequencing with an Ion 540 Chef kit, an Ion 540 Chip kit, and an Ion S5 Sequencer (Thermo Fisher Scientific).

overall_design: The whole transcripts were amplified from total cells of tumor tissue in Colon26-bearing mice and those transcripts were used to generate the 5’end Serial Analysis of Gene Expression (SAGE)-sequencing libraries. The sequencing was performed by using an Ion 540 Chef kit, an Ion 540 Chip kit, and an Ion S5 Sequencer (Thermo Fisher Scientific) according to the manufacturer’s instructions except the input library concentration was 65 pM. .

first: Chang-Yu

first: Satoshi

last: Ueha

first: Yoshiro

last: Ishiwata

first: Shoji

last: Yokochi

first: De

last: Yang

first: Joost

last: Oppenheim

first: Haru

last: Ogiwara

first: Shungo

last: Deshimaru

first: Shigeyuki

last: Shichino

first: Shiro

last: Shibayama

first: Kouji

last: Matsushima


title: Bulk population RNA-sequencing of sorted stromal cell populations from murine mammary tumours

city: London

first: James

last: Opzoomer

address: 72 Huntley Street

institute: University College London

summary: Bulk cell population transcriptomic profiling of sorted stromal cell populations from mouse mammary PyMT adenocarcinomas

overall_design: Five replicates of FACs sorted stromal cell populations from five independent 750mm3 volume MMTV-PyMT mammary adenocarcinoma tumours from five individual mice, all sample libraries were pooled and sequenced across three lanes of an Illumina HiSeq 2500 in rapid mode.

middle: W

last: Arnold


title: Gene expression analysis in HLHS iPSCs, iPSC-derived cardiac progenitors and cardiomyocytes

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

institute: Klinikum rechts der Isar – Technical University Munich

summary:
In the present study, genome-wide expression profiling (RNA-Seq) was carried out to identify genes dysregulated during cardiac differentiation of HLHS iPSCs.
Transcriptional profiling by RNASeq of three control and three HLHS iPSC lines was performed at various times during differentiation towards cardiac progenitors (CPCs) at D0, D1, D2, D3 and towards cardiomyocytes (CMs) at D6, D8, D14.

overall_design: RNA from three control and HLHS iPSC lines differentiated into CPCs and CMs in three independent differentiation experiments in triplicates was isolated at D0, D1, D2, D3, D6, D8 and D14, pooled and subjected to RNA-Seq.

first: Alessandra

last: Moretti


title: Transcriptomic analysis of natural killer (NK) cells after co-culture with RPMI 8226 multiple myleoma cell line in the presence or absence of peripheral blood lymphocytes

city: Pamplona

first: Aintzane

last: Zabaleta

state: Navarra

address: Avda. Pío XII 55

country: Spain

institute: FOUNDATION FOR APPLIED MEDICAL RESEARCH

summary:
Isatuximab is an IgG1 antibody that recognizes CD38 molecule on the surface of MM plasma cells and induces, among others, NK cell-mediated antibody-dependent cell-mediated cytotoxicity (ADCC). In this study we sough to unveil the effect of anti-CD38 antibody on NK cells
We used microarrays to detail the global programme of gene expression underlying the differences among NK cells co-cultured with RPMI 8226 cells in the presence or absence of anti-CD38 antibody

overall_design: RPMI 8226 MM cell line was co-cultured with or without anti-CD38 antibody in the presence or absence of human PBLs and the effect of the antibody over FACS sorted MM cell line and NK cells was analyzed by gene expression profile

first: Bruno

last: Paiva


title: Transcriptional Analysis of Wild Type and KLF2-/- Peritoneal Macrophages

city: Cleveland

first: Mukesh

last: Jain

state: OH

address: 2103 Cornell Rd

institute: Case Western Reserve University

summary: Krüppel-like factor 2 (KLF2) is a critical regulator of monocyte activation in response to inflammatory stimuli. Here, we report transcriptomic differences in peritoneal macrophages isolated from Lysozyme M Cre (control) and myeloid-specific KLF2 knockout mice.

overall_design: Peritoneal macrophages were isolated from lysozyme M Cre (wt) and myeloid-specific KLF2 knockout (k2) mice 72 hours after thioglycolate injection. Three mice per group were used.  cDNA sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA kit and sequenced on a Illumina HiSeq 2500 platform. Reads from each sample were aligned to the mouse genome (UCSC mm10) using TopHat2 (Kim et al., 2013). Macrophage gene expression was quantitated as fragments per kilobase of transcript per million mapped reads (FPKM) using Cufflinks (Trapnell et al., 2010).

first: David

last: Sweet

first: Neelakantan

middle: T

last: Vasudevan

first: Derin

last: Tugal

first: Nikunj

last: Sharma

first: Lilei

last: Zhang

first: Chen

last: Fu

first: E

last: Chang

middle: K


title: Single cell RNA sequencing analysis of midbrain organoids with SNCA gene triplication modeling key features of synuclienopathy

city: Montreal

first: Rhalena

middle: Amber

last: Thomas

state: QC

address: 3801 rue University, Montreal Neurological Institute, NW B150

department: Neurology

institute: McGill University

summary: SNCA, the first gene associated with Parkinson’s disease, encodes the α-synuclein protein, the predominant component within pathological inclusions termed Lewy bodies. We use 3D midbrain organoids, differentiated from human induced pluripotent stem cells derived from patients carrying a triplication of the SNCA gene and from CRISPR/Cas9 corrected isogenic control iPSCs. These human midbrain organoids recapitulate key features of α-synuclein pathology observed in the brains of patients with synucleinopathies. We used single cell RNA sequencing  to characterize the cell types within these organoids.  We find an equal proportion of neuronal and glial cells.  The neuronal populations consist of dopmainergic, excitatory and inhibitory neurons in early and late stages of maturation as well as neural precursor cells.  The glial populations consist of dividing radial glia, radial glia, astrocytes and early oligodendorcytes.

overall_design: Single cell RNA sequencing transcriptomes of midbrain organoids 165 days in shaking cultures.  Two sequencing libraries one for each genotype, each sample is 3 midbrain organoids pooled and dissociated.

first: Nguyen-Vi

last: Mohamed

first: Thomas

last: Durcan


title: Genetic and functional analysis of archaeal ATP-dependent RNA ligase in ribosomal RNA biogenesis

status: Public on Nov 01 2021

city: Tsukuba

first: Kiong

last: Ho

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary: In this study, we generated allelic knockouts of ATP-dependent RNA ligase (Rnl) in hyperthermophilic archaeon T. kodakarensis and analyze the total and small RNA by RNA-Seq.

overall_design: Knocked out the TK1545 gene by homologous recombination, and prepared RNA samples for whole transcriptosome and small RNA seq analysis. The differentially expressed genes between the two strains were analyzed.

first: Yancheng

last: Liu

first: Yuko

last: Takagi

first: Milyadi

last: Sugijanto

first: Kieu Duong My

last: Nguyen

first: Akira

last: Hirata

first: Hitoshi

last: Hoiri


title: TCOF1 DRIVES STEMNESS OF TRIPLE-NEGATIVE BREAST CANCER THROUGH KIT

first: Rebecca Y. M.

last: Chin

address: To Yuen Street

department: BMS

institute: City University of Hong Kong

summary: Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with poor prognosis. The high malignancy of TNBC is contributed by its heterogeneity and enrichment of cancer stem cells. By performing multiomic profiling, we recently uncovered super-enhancer heterogeneity between breast cancer subtypes. Here, we identify TCOF1 as a novel super-enhancer-regulated gene that promotes TNBC growth and stemness. TCOF1, which plays a critical role in craniofacial development, is frequently upregulated in TNBC and its elevated expression correlates with shorter overall survival. Whereas TCOF1 depletion has potent effects on the growth and stemness of basal-like TNBC, it has no effect on mesenchymal-like cells, highlighting the distinct molecular dependency in different subgroups of TNBC. Whole genome RNA sequencing uncovers several stem cell molecules regulated by TCOF1. We further demonstrate that the upregulation of KIT by TCOF1 mediates TNBC stemness. These findings provide a rationale for developing therapeutics targeting TCOF1 in basal-like TNBC.

overall_design: Examination of mRNA profiles of MDA-MB-468 mammosphere with or without TCOF1 knockout

first: Rebecca


title: Transcriptomics and chromatin alterations - Septal lncRNA Meg3 is involved in social fear in mice

city: Rehovot

first: Igor

last: Ulitsky

state: Central

address: 234 Hertzl St.

country: Israel

institute: Weizmann Institute of Science

summary: Social anxiety disorder is characterized by a persistent and abnormal fear and avoidance of social situations, but available treatment options are rather unspecific. Using an established mouse social fear conditioning (SFC) paradigm, we profiled gene expression and chromatin alterations after acquisition and extinction of social fear within the septum, a brain region important for social fear and social behaviors. We validated coding and non-coding RNAs and found specific isoforms of the long non-coding RNA Meg3 to be regulated depending on the success of social fear extinction. In vivo knockdown of specific Meg3 isoforms in conditioned mice resulted in impaired social fear extinction, as revealed by lower social investigation levels at the end of the extinction training, accompanied with increased baseline activity of the PI3K/AKT signaling pathway. Using ATAC-Seq and CUT&RUN, we characterized alterations in chromatin level after social fear extinction and identified Auts2 and Dclk3 as potential targets of Meg3.

overall_design: RNA-seq, ATAC-Seq and Cut&Run for H3K27me3 in mouse brain septum

first: Melanie

last: Royer

first: Balagopal

last: Pai

first: Rohit

last: Menon

first: Anna

last: Bludau

first: Katharina

last: Gryksa

first: Rotem

middle: B

last: Perry

first: Gunter

last: Meister

first: Inga

last: Neumann


title: Global transcriptome profiling in peripheral blood mononuclear cells identifies dysregulation of immune processes in individuals with radiologically isolated syndrome

city: Moscow

first: Maxim

last: Kozin

address: Ostrovitanova 1

country: Russia

institute: Pirogov Russian National Research Medical University

summary: The presence of brain/spinal white matter lesions typical for multiple sclerosis (MS) in asymptomatic individuals is known as ‘radiologically isolated syndrome’ (RIS). Allow for the established fact that RIS patients are at high risk of MS development, understanding the causes underlying RIS onset and the variability of its conversion to MS are of great importance. In order to investigate RIS-specific transcription signature we perfromed high-throughput RNA sequencing in peripheral blood mononuclear cells (PBMCs) of 8 RIS patients and 8 age- and sex-matched healthy controls. We identified 57 differentially expressed genes (DEGs), which levels differed by more than 2 times when compared these groups (FDR p value < 0.05). Gene ontology enrichment analysis in the "biological process" category revealed 16 signalling pathways significantly overrepresented by identified DEGs. The most significant changes in gene expression in PBMCs of RIS patients occur in pathways involved in regulation of the immune response, cytokine and chemokine signaling, cytokine production, and leukocyte migration. In general, analyzing the global transcriptome we demonstrated the dysregulation of immune processes in PBMCs of RIS patients, confirming the current assumption that RIS represents the preclinical stage and/or subclinical form of MS.

overall_design: We performed RNA-seq in peripheral blood mononuclear cells of 8 radiologically isolated syndrom (RIS) patients and 8 healthy controls (HC).

first: Natalia

last: Baulina

first: Ivan

last: Kiselev


title: 10x Genomics single cell RNA-sequencing of sorted CD45+ Ly6G- CD11b+ F4/80+ tumour-associated macrophages from murine mammary tumours

first: James

last: Opzoomer

summary: Singe-cell transcriptomic profiling of sorted tumour-associated macrophage cells from mouse mammary adenocarcinomas

overall_design: Three replicates of FACs sorted tumour-associated macrophages from three independent 750mm3 volume MMTV-PyMT mammary adenocarcinoma tumours from three individual mice.

first: Joanne

middle: E

last: Anstee

last: Arnold


title: Cocaine/saline study in HMDP mouse strains of PFC/NAc

city: Los Angeles

first: Desmond

middle: J

last: Smith

address: 650 Charles E Young Drive South

institute: UCLA

summary: This project will chart with high-resolution the genetic pathways that give rise to defined clinical phenotypes related to cocaine addiction. We will utilize the power of the hybrid mouse diversity panel (HMDP), combined with high quality behavioral phenotyping and massive-scale RNA sequencing, to trace the interconnections from DNA to RNA to clinical trait and provide layered information on the mechanisms of cocaine abuse. The HMDP consists of 100 inbred and recombinant inbred strains and has a wide array of meiotic breakpoints. The panel has been densely genotyped with more than 200,000 single nucleotide polymorphisms (SNPs), allowing very fine mapping of quantitative trait loci (QTLs). Further, the HMDP is genetically stable and renewable and can be assayed for multiple phenotypes, yielding cumulative biological information. We will expand our previous HMDP-based studies of cocaine abuse-related traits by adding massive-scale RNA sequencing (RNA-Seq), in order to detail the genetic control of the pathways to addiction.

overall_design: Use of hybrid mouse diversity panel to map genetic pathways related to cocaine addiction

middle: D

last: Jentsch

first: Arshad

middle: H

last: Khan


title: Isoforms of SEMA3E-containing supernatant treated gene expression in human aortic endothelial cells

city: Shanghai

first: Ruiting

last: Li

state: Shanghai

address: 600 Yishan Rd

institute: Shanghai Sixth People's Hospital

summary: The expression of SEMA3E isoforms changes in mouse circulation with type 1 diabetes. The alterations in the transcriptional profiles of human aortic endothelial cells (HAECs) in response to PCS1 (Processing consensus sequences)-cleaved SEMA3E and PCS1-uncleaved SEMA3E were examined.

overall_design: HAECs were assigned to three groups and treated with conditioned media containing PCS1-cleaved SEMA3E (S), PCS1-uncleaved SEMA3E (L) and RFP (C) respectively for six hours. The gene expression profiling in the treated HAECs were analyzed by RNA-seq.

first: Jungong

last: Zhao


title: HBx increases chromatin accessibility and ETV4 expression to regulate Dishevelled-2 and promote HCC progression

city: Nanjing

first: Chuqian

last: Zheng

state: Jiangsu

address: 87 Dingjiaqiao, Gulou District

department: Department of Medical Genetics and Developmental Biology, School of Medicine

institute: Southeast University

summary:
Purpose: The goals of this study are to invsetigate the primary biological process of HBx.
Methods: Briefly, samples (L02 cells transfected with pcDNA4.0-vector or pcDNA4.0-HBx) were used to extract total RNAs for quality control and RNA-seq loading samples. RNA-seq was performed as DGE on an Illumina platform and 50 bp paired-end reads were generated (Guangzhou Epibiotek Co.,Ltd.).
Results: Negative regulation of transferase activity was identified as the primary biological process according to the gene ontology (GO) analysis. TNF signaling pathway was identified as the primary biological processes according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis . DNA binding transcription factor activity was identified as the primary biological processes according to the gene set enrichment analysis (GSEA).
Conclusions: RNA-seq in L02 cell lines revealed that HBx mainly regulated the DNA binding transcription factor activity.

overall_design: mRNA profiles of L02-vector and L02-HBx cells


title: MICROBIOTA-DERIVED ACETATE ENABLES THE METABOLIC FITNESS OF THE CNS INNATE IMMUNE SYSTEM DURING HEALTH AND DISEASE

first: Daniel

last: Erny

address: Breisacher Str. 64

department: Neuropathology

institute: University hospital Freiburg

summary: As tissue macrophages of the central nervous system (CNS) microglia constitute the pivotal immune cells of this organ. Microglial features are strongly dependent on environmental cues such as commensal microbiota. Gut bacteria are known to continuously modulate microglia maturation and function by the production of short-chain fatty acids (SCFA). However, the precise mechanism of this crosstalk is unknown. Here we determined that the immature phenotype of microglia from germ-free (GF) mice is epigenetically imprinted by H3K4me3 and H3K9ac on metabolic genes associated with substantial functional alterations including increased mitochondrial mass and specific respiratory chain dysfunctions. We identified acetate as the essential microbiome-derived SCFA driving microglia maturation and regulating the homeostatic metabolic state, and further showed that it is able to modulate microglial phagocytosis and disease progression during neurodegeneration. These findings indicate that acetate is an essential bacteria-derived molecule driving metabolic pathways and functions of microglia during health and perturbation.

overall_design: we compared microglia from mice housed under germ-free and specific-pathogen-free conditions. In addition, a group of mice was treated with acetate via the drinking water.

first: Nikolaos

last: Dokalis

first: Charlotte

last: Mezö

first: Angela

last: Castoldi

first: Omar

last: Mossad

first: Ori

last: Staszewski

first: Maximilian

last: Frosch

first: Matteo

last: Villa

first: Vidmante

last: Fuchs

first: Arun

last: Mayer

first: Jana

last: Neuber

first: Janika

last: Sosat

first: Stefan

last: Tholen

first: Oliver

last: Schilling

first: Andreas

last: Vlachos

first: Thomas

last: Blank

first: Merceds

last: Gomez de Agüero

first: Andrew

last: Macpherson

first: Edward

last: Pearce

first: Marco

last: Prinz


title: Leptin Signalling in the Ovary of Diet-Induced Obese Mice Regulates Activation of Nod-Like Receptor Protein 3 Inflammasome

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: Obesity leads to ovarian dysfunction and the establishment of local leptin resistance. The aim of our study was to characterise levels of Nod-Like Receptor Protein 3 (NLRP3) inflammasome activation during obesity progression in the mouse ovaries and liver and test the putative role of leptin on its regulation. C57BL/6J mice were treated with equine chorionic gonadotropin (eCG) or human chorionic gonadotropin (hCG) for oestrous cycle synchronisation and ovaries collection. In diet-induced obesity (DIO) model, mice were fed chow diet (CD) or high fat diet (HFD) for 4 or 16 weeks (wk), whereas in hyperleptinemic model (LEPT), mice were injected with leptin for 16 days (16L) or saline (16C) and in the genetic obese leptin-deficient ob/ob (+/? and -/-) animals were fed CD for 4wk. Either ovaries and liver were collected, as well as cumulus cells (CCs) after superovulation from DIO and LEPT. In DIO protocol, protein expression of NLRP3 inflammasome components was increased in 4wk HFD, but decreased in 16wk HFD. Moreover LEPT and ob/ob models revealed NLRP3 and IL-1 upregulation in 16L and downregulation in ob/ob. Transcriptome analysis of CC showed common genes between LEPT and 4wk HFD modulating NLRP3 inflammasome. Moreover analysis in the liver showed upregulation of NLRP3 protein only after 16wk HFD, but also the downregulation of NLRP3 protein in ob/ob-/-. We showed the link between leptin signalling and NLRP3 inflammasome activation in the ovary throughout obesity progression in mice, elucidating the molecular mechanisms underpinning ovarian failure in maternal obesity.

overall_design: A total of 34 samples were analyzed including 3 from leptin treatment controls, 5 from leptin treated, 5 chow diet fed for 4 weeks, 5 high-fat diet fed for 4 weeks, 6 chow diet fed for 16 weeks, 7 high-fat diet fed for 16 weeks, and 3 low weight gainers after high-fat diet for 16 weeks.

first: Marek

last: Adamowski

first: Karolina

last: Wołodko

first: Joana

last: Oliveira

first: Juan

last: Castillo-Fernandez

first: Daniel

last: Murta

first: Gavin

last: Kelsey

first: António

middle: M

last: Galvão


title: Rewiring of gene networks underlying mite allergen-induced CD4 + Th-cell responses during immunotherapy

city: Nedlands

first: Anya

last: Jones

state: Western Australia

address: Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue

country: Australia

institute: Telethon Kids Institute, The University of Western Australia

summary:
Background: Multiple regulatory mechanisms have been identified employing conventional hypothesis-driven approaches as contributing to allergen-specific immunotherapy outcomes, but understanding of how these integrate to maintain immunological homeostasis is incomplete.

Objective: To explore the potential for unbiased systems-level gene co-expression network analysis to advance understanding of immunotherapy mechanisms.

Methods: We profiled genome-wide allergen-induced Th-cell responses prospectively during 24 months subcutaneous immunotherapy (SCIT) in 25 rhinitis, documenting changes in immunoinflammatory pathways and associated co-expression networks and their relationships to symptom scores out to 36 months.

Results: Prior to immunotherapy, mite-induced Th-cell response networks involved multiple discrete co-expression modules including those related to Th2-, type1 IFN-, inflammation- and FOXP3/IL2-associated signalling. A signature comprising 109 genes correlated with symptom scores, and these mapped to cytokine signalling/T-cell activation-associated pathways, with upstream drivers including hallmark Th1/Th2- and inflammation-associated genes. Reanalysis after 3.5 months SCIT updosing detected minimal changes to pathway/upstream regulator profiles despite 32.5% symptom reduction; however, network analysis revealed underlying merging of FOXP3/IL2-with inflammation-and Th2-associated modules. By 12 months SCIT, symptoms had reduced by 41% without further significant changes to pathway/upstream regulator or network profiles. Continuing SCIT to 24 months stabilized symptoms at 47% of baseline, accompanied by upregulation of the type1 IFN-associated network module and its merging into the Th2/FOXP3/IL2/inflammation module.

Conclusions: Subcutaneous immunotherapy stimulates progressive integration of mite-induced Th cell-associated Th2-, FOXP3/IL2-, inflammation- and finally type1 IFN-signalling subnetworks, forming a single highly integrated co-expression network module, maximizing potential for stable homeostatic control of allergen-induced Th2 responses via cross-regulation. Th2-antagonistic type1 IFN signalling may play a key role in stabilizing clinical effects of SCIT.

overall_design: A total of n=198 samples were profiled by microarray comparing 24h HDM culture with medium control prior to SCIT (visit V1, n=25) and during immunotherapy at visits V2 (3.5mths, n=25), V4 (12mths, n=25) and V5 (24mths, n=24).

middle: C

first: Denise

last: Anderson

first: Niamh

last: Troy

first: Dom

last: Mallon

first: Michael

last: Serralha

first: Barbara

last: Holt

first: Anthony

last: Bosco

first: Patrick

middle: G


title: Transcriptome profiling of gut CD8 tissue-resident T cells.

city: Utrecht

first: Lisanne

last: Lutter

address: Lundlaan 6

country: Netherlands

institute: University Medical Center Utrecht

summary: We investigated the transcriptomic landscape of human CD8 tissue-resident T cells (Trm) derived from the ileum to study the differences in compartment (epithelium and lamina propria), CD103+ and CD103- Trm and inflammation-induced changes (active Crohn's disease vs healthy controls).

overall_design: Examination of the transcriptomic CD8 tissue-resident profile (both CD69+CD103+ and CD69+CD103-) in the epithelium and lamina propria of the terminal ileum in both Crohn's disease patients and healthy controls.

first: Femke

last: van Wijk


title: Ablation of TET proteins in adipocytes protects against adiposity and metabolic dysfunction by potentiating energy expenditure

city: Ulsan

first: Sung Ho

last: Park

address: 50, UNIST-gil

institute: UNIST

summary: Ten-eleven translocation (TET) proteins oxidize 5-methylcytosine in DNA to 5- hydroxymethylcytosine and further oxidized derivatives. Here we show that TET proteins are key epigenetic suppressors of adipocyte thermogenesis and energy expenditure in both white and brown adipose tissues in vivo. Tet expression in adipocytes decreases upon cold or adrenergic stimulation but increases following high-fat diet (HFD) consumption. Mice with triple deletion of all three Tet genes in adipocytes have higher energy expenditure due to enhanced fat browning and thermogenesis. They also show significantly enhanced lipolysis because of elevated expression of Adrb3 and key lipases including Atgl and Hsl. Consequently, the knockout mice display improved cold tolerance and are substantially resistant to obesity, inflammation, and associated metabolic complications including insulin resistance. Mechanistically, TET deficiency substantially prevents the HFD-induced transcriptional alterations in adipose tissues. TET proteins recruit histone deacetylases (HDACs) to the key thermogenic gene loci including Adrb3, Ppargc1a, and Ucp1, leading to transcriptional repression through histone deacetylation. Thus, the TET-HDAC axis may be therapeutically targeted to treat obesity and related metabolic diseases.

overall_design: Analysis of transcriptional changes in mouse adipocytes (WT, TET KO)

first: S


title: Treatment of p-EMT prostate cancer cells with the demethylating drug 5-azacytidine reduces cell aggressiveness and changes methylation profile.

first: jenna

last: kitz

state: Ontario

address: 305 Central Ave, Unit 1

department: Anatomy and Cell Biology

institute: Western University

type: Methylation profiling by genome tiling array

summary: p-EMT prostate cancer cells with EMT inducing transcription factor Zeb1 knocked down show increased aggressiveness compared to completely epithelial or mesenchymal controls. Treatment of aggressive p-EMT cells with the demethylating agent 5-azacytidine decreases cell aggressiveness which is corrlated with changes in the methylation profile of cancer silencing genes.

overall_design: Control and Zeb1 KD pc-3 cancer cells were treated with either DMSO or 5-azacytidine and assessed for changes in methylation of cancer silencing genes to create a p-EMT cancer screening expression profile panel.

first: Jenna

last: Kitz

first: Alison

last: Allan


title: miRNA expression profile in calcium oxalate (CaOx) nephrocalcinosis model.

city: Wuhan

first: Haoran

last: Liu

state: Hubei

address: Jiefang avenue 1095

department: Urology

country: China

institute: Tongji Hospital

summary: Microarray analysis was used to assess the expression levels of miRNAs in six pairs of kidney tissues of calcium oxalate (CaOx) nephrocalcinosis mouse model and normal mouse kidney tissues.The animals used in the experiment were male 6-8 weeks old C57BL/6J mice. To establish a CaOx nephrocalcinosis mouse model, each mouse was intraperitoneally injected with saline or glyoxylate acid (Gly) (75 mg/kg/d, 200 μl) from day 1 to day 7. Animals were euthanized after 7 days, and kidney samples were collected at the time of euthanasia.

overall_design: MiRNA expression profile in six pairs of kidney tissues of calcium oxalate (CaOx) nephrocalcinosis mouse and wild type mouse.

first: Xiaoqi

last: Yang

first: Chen

last: Duan

first: Tao

last: Ye

first: Xiangyang

last: Yao

first: Peng

last: Lv

first: Bo

last: Li

first: Zhangqun

first: Hua

last: Xu


title: Long noncoding RNA expression profiles in brain ischemic tolerance by cerebral ischemic preconditioning

city: Shijiazhuang City

first: Min

last: Zhang

address: 361 Zhongshan East Road, Shijiazhuang, 050017, People’s Republic of China

institute: Hebei Medical univercity

summary: In this study, cerebral cortical astrocytes and neurons of rats were co-cultured, the astrocytes of the co-cultured cell model pretreated by ischemic preconditioning (45 min of OGD) were subjected to lncRNA high-throughput sequencing (RNA-seq).

overall_design: Cortical astrocytes lncRNA profiles of ischemic preconditioning (45 min of OGD) and control group

first: Shichao


title: Reorganization of Mitochondrial Respiratory Supercomplexes Induces Myoblasts Differentiation

city: Beijing

first: Haining

last: Wang

address: Jia 3 Datun Road

institute: Institute of Zoology, Chinese Academy of Science

summary: The existence of respiratory supercomplexes (SCs) has been well acknowledged especially with the development of cryo-EM in the past few years, but their physiological relevance remains elusive. Dynamics of OXPHOS complexes is tightly correlated to cell fate switch, but whether SCs involve in this process is unknown. During C2C12 myogenesis, CIII2 and CIV as well as the subunits of CIII and CIV were slightly increasing, while SC III2+IV was decreasing, which indicates that SC reorganization may regulate myogenesis. Knockdown Cox7a2l decreased SCs III2+IV, I+III2+IV2 and I+III2+IV3, but had little effect on I+III2+IV. Transcriptome and quantitative-proteome analysis indicated that Cox7a2l silence activated myogenic gene expression and repressed cell cycle-associated gene expression. Besides, knockdown of Cox7a2l decreased CII abundance and accumulated succinate, which in turn suppressed certain key transcription factors, such as HMGA1 which is important for stemness maintenance. Our results indicated that respiratory supercomplex reorganization changed succinate homeostasis and myogenesis related gene expression profiles, thus switching cell fate.

overall_design: RNA-seq of C2C12 cells treated with random control siRNA or targeted-Cox7a2l siRNA.

first: Man

last: Cheng

first: Shaofan

last: Han


title: Detection of duplication mutations in coding regions in normal lung and lung tumor in wild-type (WT) and FEN1 A159V mutant mice

city: Duarte

first: wei

last: chen

state: CA

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

country: USA

institute: City of Hope National Medical Center

type: Genome variation profiling by high throughput sequencing

summary: Faithful and efficient Okazaki fragment maturation is the key to maintain the genome integrity. In addition, this process is coupled with deposition of histone proteins. Therefore, functional deficiency in Okazaki fragment maturation may cause duplication mutations. We conduct WES of normal lung and lung tumor from WT and A159V/WT mice to define the duplication mutations caused by defective Okazaki fragment maturation.

overall_design: We conduct whole exosome sequencing of the normal lung and tumor lung from WT and FEN1-A159V/WT mice (n=1 for each sample). We use Pindel to define the genome-wide duplication mutations frequency in the coding regions caused by defective Okazaki fragment maturation.

first: Li

last: Zheng

first: Zhaohui

last: Gu

first: Xiwei

last: Wu

first: Binghui

last: Shen


title: Transcriptomic responses to iron bioavailability from virus-mediated lysates in marine prokaryotes

city: Vancouver

first: Anwar

last: Alqattan

state: BC

address: 4200-6270 University Boulevard

department: Earth Ocean and Atmospheric Sciences/Oceanography

country: Canada

institute: University of British Columbia

summary:
Previous studies have demonstrated that the iron content in marine heterotrophic bacteria is comparatively higher than that of phytoplankton. Therefore, they have been indicated to play a major role in the biogeochemical cycling of iron. In this study, we aimed to investigate the potential of viral lysis as a source of iron for marine heterotrophic bacteria. Viral lysates were derived from the marine heterotrophic bacterium, Vibrio natriegens PWH3a (A.K.A Vibrio alginolyticus). The bioavailability of Fe in the lysates was determined using a model heterotrophic bacterium, namely, Dokdonia sp. strain Dokd-P16, isolated from Fe-limited waters along Line P transect in the Northeastern Pacific Ocean. The bacteria were grown under Fe-deplete or Fe-replete conditions before being exposed to the viral lysate. Differential gene expression following exposure to the viral lysate was analyzed via RNA sequencing to identify differentially expressed genes under iron-replete and iron-deplete conditions. This study would provide novel insights into the role of viral lysis in heterotrophic bacteria in supplying bioavailable iron to other marine microorganisms under iron-limiting and non-limiting conditions.
First, the marine heterotrophic bacterium genome, Dokdonia sp. strain Dokd-P16, was sequenced to provide a genomic context for the expression studies. Subsequently, the relative gene expression in Dokdonia sp. strain Dokd-P16 grown under Fe limiting and non-limiting conditions were analyzed. This transcriptomic approach would be utilized to elucidate genes regulated by Fe availability in Dokdonia sp. strain Dokd-P16, which indicate its Fe-related response viral lysate exposure. Taken together, in this study, the transcriptomic responses of Fe-limited and non-limited marine heterotrophic bacteria were analyzed, which provided novel insights into the biological availability of Fe from the viral lysates.

overall_design: Samples grown under either Fe-deplete or Fe-replete conditions then exposed with either viral lysate (L) media control (AQUIL) for five different exposure times (T0,T1,T2,T3,T4). An additional control with nothing added (NOADD) is also included and sampled at two different time points (Tm,Tend). All combinations of Fe condition, exposure and time were replicated five times for a grand total 120 samples (2 Fe conditions X 2 exposures X 5 time points + 2 Fe conditions X 1 exposure X 2 time points).

last: Al-Qattan

first: Curtis

last: Suttle

first: Maria

last: Maldonado


title: Transcriptional Characterization of healthy optic nerve

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

overall_design: MACE RNA sequencing of 4 human healthy optic nerve specimens

first: Julian

last: Wolf


title: RNAseq of human retinal pigment epithelial cells/choroid

city: Melbourne

first: Raymond

middle: Ching-Bong

last: Wong

state: VIC

address: Level 7 Smorgan Family Wing, 32 Gisborne St

institute: Centre for Eye Research Australia Ltd/ University of Melbourne

summary: We report the RNAseq dataset of retinal pigmented epithelium/choroid samples extracted from 3 post-mortem heathy human retinas.

overall_design: The retinal pigment epithelial cells/choroid layers were dissected from donor retinas and processed for RNA extraction using the Rneasy kit with Dnase I (Qiagen). RNA quality was checked using bioanalyzer and transcriptome libraries were prepared using the TruSeq Stranded mRNA kit (Illumina) and processed for 100bp single-end sequencing with an Novaseq 6000 (Illumina), which yieled ~38-50 million reads per sample.


title: Gene expression data of  the liver in hepatocyte-specific Phgdh knockout mice

city: Fukuoka

first: Shigeki

last: Furuya

address: 6-10-1, Hakozaki, Higashi-ku

country: Japan

institute: Kyushu University

summary:
Live hepatocyte-specific Phgdh KO (LKO) mice were generated by introducing Albumin-Cre transgene into Phgdh flox/flox (Floxed) mice.
LKO mice exhibited mild obesity and impaired glucose intolerance at 30 weeks old.

overall_design: Total RNA was extracted from the liver of LKO and littermate Floxed mice (male, 30 weeks old, n = 6, each genotype) . Six biological replicates for each treatment were used for amplification and labeling for Agilent microarray platform.

first: Momoko

last: Hamano


title: Next-generation sequencing facilitates quantitative analysis of rat BMSCs in fast, medium or slow stress relaxation SA hydrogel

city: Chongqing

first: chuanchuan

last: lin

state: China

address: Shayang Road, Shapingba distract,

institute: Chongqing University

summary: To identify genes and the molecular pathways involved in the regulation of mesenchymal stem cells (MSCs) exposure to various matrix viscoelasticity, we performed RNA-sequence of MSCs in fast stress relaxation (FAST), medium stress relaxation (MEDIUM) and slow stress relaxation (SLOW) matrix.

overall_design: mRNA profiles of MSCs in FAST, MEDIUM and SLOW group (48 h) were generated by deeping sequencing, using Illumina HiSeq2000.

first: Kaiyong

last: Cai

first: Chuanchuan

last: Lin


title: Transcriptional Characterization of healthy eye lid

overall_design: MACE RNA sequencing of 6 human healthy eye lid specimens


title: Venetoclax treatment imparts distinct cell death sensitivity and adaptivity patterns in T cells

city: Chicago

first: James

last: LaBelle

state: IL

address: 900 East 57th Street, KCBD 5122

institute: University of Chicago

summary: BH3 mimetics are increasingly used as anti-cancer therapeutics either alone or in conjunction with other chemotherapies. However, mounting evidence has also demonstrated that BH3 mimetics induce varied amounts of cell death in healthy immune populations. In order to maximize their clinical potential, it is essential to understand how BH3 mimetics affect discrete immune populations and to determine how BH3 mimetic pressure causes immune system adaptation. Here we focus on the BCL-2 specific inhibitor venetoclax (ABT-199) and its effects following short-term and long-term BCL-2 blockade on T cell subsets. Seven day "short-term” ex vivo and in vivo BCL-2 inhibition led to divergent cell death sensitivity patterns in CD8+ T cells, CD4+ T cells, and Tregs resulting in shifting of global T cell populations towards a more memory T cell state with increased expression of BCL-2, BCL-XL, and MCL-1. However, twenty-eight day “long-term” BCL-2 blockade during T cell engraftment following bone marrow transplantation did not lead to changes in the global T cell landscape. Despite the lack of changes in T cell proportions, animals treated with venetoclax developed CD8+ and CD4+ T cells with high levels of BCL-2 and were more resistant to apoptotic stimuli. Further, we demonstrate through RNA profiling that T cells adapt while under BCL-2 blockade post-transplant and develop a more activated genotype. Taken together, these data emphasize the importance of evaluating how BH3 mimetics affect the immune system in different treatment modalities and disease contexts and suggest that venetoclax should be further explored as an immunomodulatory compound.

overall_design: RNA-seq of naïve CD8+ T cells and CD4+ T cells following 28 days of daily treatment with venetoclax in T-cell depleted bone marrow transplanted mice.


title: A Hybrid Nanofiber/Paper Cell Culture Platform for Building a 3D Blood-brain Barrier Model

city: Indiana

first: Lane

middle: A

last: Baker

state: IN

address: Indiana University 800 E Kirkwood Ave

department: Chemistry

institute: Indiana University

summary: The blood brain barrier (BBB) protects the central nervous system from toxins and pathogens in the blood by regulating permeation of molecules through the barrier interface. In vitro BBB models described to date reproduce some aspects of BBB functionality, but also suffer from incomplete phenotypic expression of brain endothelial traits, difficulty in reproducibility and fabrication, or overall cost. To address these limitations, we describe a three-dimensional (3D) BBB model based on a hybrid paper/nanofiber scaffold. The cell culture platform utilizes lens paper as a framework to accommodate 3D culture of astrocytes. An electrospun nanofiber layer is coated onto one face of the paper to mimic the basement membrane and support growth of an organized two-dimensional layer of endothelial cells (ECs). Human induced pluripotent stem cell-derived ECs and astrocytes are co-cultured to develop a human BBB model. Morphological and spatial organization of model are validated with confocal microscopy. Measurements of transendothelial resistance and permeability demonstrate the BBB model develops a high-quality barrier and responds to hyperosmolar treatments. RNA-sequencing shows introduction of astrocytes both regulates EC tight junction proteins and improves endothelial phenotypes related to vasculogenesis.  This model shows promise as a model platform for future in vitro studies of the BBB.

overall_design: The samples for RNA sequencing include stem cell-derived endothelial cells in triplicates, stem cell-derived astrocytes in triplicates, and the assembled BBB models in triplicates. 9 samples in total were analyzed.

first: Kaixiang

last: Huang

first: Andre

last: Castiaux

first: Ram

last: Podicheti

first: Douglas

last: Rusch

first: R

middle: S

last: Martin


title: Tumor-suppressive and tumor-promoting roles of cancer-associated fibroblast-released mediators in desmoplastic liver metastasis

city: NEW YORK

first: Robert

last: Schwabe

state: NY

address: 1130 St. Nicholas Ave

department: Medicine

institute: COLUMBIA PRESBYTERIAN MED CTR

summary: Here we analyzed mouse derived samples to investigate origin, subtypes, functions and cell-cell interactions of cancer-associated fibroblasts in desmoplastic liver metastasis. Hepatic stellate cell-derived cancer-associated fibroblasts were isolated from three different models of liver metastasis induced by intra-splenic injection of cell lines Panc02, KPCY and CMT93 and analyzed by bulk RNA sequencing. In addition, CAF from Panc02- and CMT93-induced liver metastasis were analyzed by single cell sequencing.

overall_design: Bulk RNA sequencing was performed in 9 samples: 1 isolate of quiescent mouse hepatic stellate cells (HSC); 3 isolates of HSC-derived CAF from Panc02; 3 isolates of HSC-derived CAF from KPCY and 2 isolates of HSC-derived CAF from CMT93. Mouse HSC were isolated by in situ liver perfusion as previously described, the cells were further purified by FACS using endogenous retinoid fluorescence and/or by LRAT-Cre-induced TdTomato fluorescence. CAFs from Lrat-Cre+ TdTom+ Col1a1-GFP+ mice were isolated from tumors following the HSC protocol with few modifications. Before FACS sorting, cells were subjected to a separation gradient using Nycodenz 34%. CAF were sorted for Col1a1-induced GFP; HSC-derived CAFs were sorted by Col1a1-induced GFP and TdTomato double positive signal. Single-cell RNA-sequencing was performed in 2 samples: one sample of CAF-enriched cells isolated from Panc02 and one sample of CAF-enriched cells isolated from CMT93. CAF were obtained by digesting livers as above with an addition trypsin digestion. Enriched CAF were obtained by sorting cells expressing high levels of Col1a1-induced GFP, followed by addition of a small fraction of unpurified cells. All cell sorting was performed on a BD Aria II Cell Sorter, followed by RNA sequencing or scRNA sequencing. For bulk RNA sequencing, purified HSC and HSC-CAF freshly isolated and never cultured, RNA was extracted using the RNeasy Micro or Mini Kit (Qiagen) with on-column DNase digestion accordingly to manufacturer instructions. RNA (RNA integrity number [RIN] >8, as determined by Bioanalyzer 2100, Agilent Technologies) was used to construct libraries using Illumina TruSeq RNA Preparation Kit according to the manufacturer’s instructions. For single-cell RNA sequencing, CAF-enriched samples containing multiple cell populations were acquired by combining Col1a1-GFP+ cells (70%) with the entire live cell population (30%) after sorting on a BD Aria II Cell Sorter. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ v3 Reagent Kit (10x Genomics) according to manufacturer’s instructions. 12 cycles of cDNA amplification and 12 cycles of library amplification were performed, and samples were sequenced on an Illumina NovaSeq 6000 Sequencing System.

first: Sonakshi

last: Bhattacharjee

first: Maximilian

last: Miller